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- PDB-6txs: The structure of the FERM domain and helical linker of human moes... -

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Basic information

Entry
Database: PDB / ID: 6txs
TitleThe structure of the FERM domain and helical linker of human moesin bound to a CD44 peptide
Components
  • CD44 antigen
  • Moesin
KeywordsPROTEIN BINDING / PIP / FERM domain / Alzheimer's disease / CD44
Function / homology
Function and homology information


positive regulation of monocyte aggregation / regulation of lymphocyte migration / T cell aggregation / regulation of organelle assembly / Hyaluronan degradation / positive regulation of early endosome to late endosome transport / membrane to membrane docking / monocyte aggregation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex ...positive regulation of monocyte aggregation / regulation of lymphocyte migration / T cell aggregation / regulation of organelle assembly / Hyaluronan degradation / positive regulation of early endosome to late endosome transport / membrane to membrane docking / monocyte aggregation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / uropod / regulation of lamellipodium morphogenesis / immunological synapse formation / gland morphogenesis / hyaluronan catabolic process / positive regulation of protein localization to early endosome / cellular response to testosterone stimulus / establishment of epithelial cell apical/basal polarity / positive regulation of heterotypic cell-cell adhesion / establishment of endothelial barrier / cartilage development / positive regulation of podosome assembly / Sensory processing of sound by inner hair cells of the cochlea / wound healing, spreading of cells / Sensory processing of sound by outer hair cells of the cochlea / leukocyte migration / leukocyte cell-cell adhesion / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / microvillus membrane / regulation of cell size / microvillus / pseudopodium / negative regulation of DNA damage response, signal transduction by p53 class mediator / Recycling pathway of L1 / lamellipodium membrane / Integrin cell surface interactions / T cell proliferation / collagen binding / cell adhesion molecule binding / T cell migration / Degradation of the extracellular matrix / cellular response to fibroblast growth factor stimulus / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / secretory granule membrane / T cell activation / cell-matrix adhesion / Cell surface interactions at the vascular wall / cell periphery / cell projection / adherens junction / filopodium / cell-cell adhesion / structural constituent of cytoskeleton / cytokine-mediated signaling pathway / Interferon gamma signaling / apical part of cell / positive regulation of protein catabolic process / Signaling by ALK fusions and activated point mutants / transmembrane signaling receptor activity / cell migration / regulation of cell shape / double-stranded RNA binding / actin binding / blood microparticle / basolateral plasma membrane / vesicle / cytoskeleton / positive regulation of ERK1 and ERK2 cascade / cell adhesion / apical plasma membrane / inflammatory response / signaling receptor binding / focal adhesion / Neutrophil degranulation / positive regulation of gene expression / protein kinase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / cell surface / Golgi apparatus / extracellular space / extracellular exosome / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin, alpha-helical domain / CD44 antigen / CD44 antigen-like / Link domain signature. ...Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin, alpha-helical domain / CD44 antigen / CD44 antigen-like / Link domain signature. / Link domain / Extracellular link domain / Link domain profile. / Link (Hyaluronan-binding) / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / C-type lectin-like/link domain superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / C-type lectin fold / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
CD44 antigen / Moesin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBradshaw, W.J. / Katis, V.L. / Kelly, J.J. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)1U54AG065187-01 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Discovery of FERM domain protein-protein interaction inhibitors for MSN and CD44 as a potential therapeutic approach for Alzheimer's disease.
Authors: Du, Y. / Bradshaw, W.J. / Leisner, T.M. / Annor-Gyamfi, J.K. / Qian, K. / Bashore, F.M. / Sikdar, A. / Nwogbo, F.O. / Ivanov, A.A. / Frye, S.V. / Gileadi, O. / Brennan, P.E. / Levey, A.I. / ...Authors: Du, Y. / Bradshaw, W.J. / Leisner, T.M. / Annor-Gyamfi, J.K. / Qian, K. / Bashore, F.M. / Sikdar, A. / Nwogbo, F.O. / Ivanov, A.A. / Frye, S.V. / Gileadi, O. / Brennan, P.E. / Levey, A.I. / Axtman, A.D. / Pearce, K.H. / Fu, H. / Katis, V.L.
History
DepositionJan 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 2.0Dec 2, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly_prop / pdbx_validate_torsion / refine / refine_ls_restr / refine_ls_shell / software / struct_mon_prot_cis
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.pdbx_formal_charge / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly_prop.value / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_number_reflns_R_work / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.solvent_model_details / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.R_factor_all / _refine_ls_shell.pdbx_fsc_free / _refine_ls_shell.pdbx_fsc_work / _refine_ls_shell.wR_factor_R_work / _software.version / _struct_mon_prot_cis.pdbx_omega_angle
Description: Model orientation/position
Details: The side chain of His288 was the wrong way round. It has now been flipped.
Provider: author / Type: Coordinate replacement
Revision 2.1Oct 25, 2023Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / citation / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 1, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 2.3Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.4Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Moesin
BBB: CD44 antigen


Theoretical massNumber of molelcules
Total (without water)42,1152
Polymers42,1152
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, A longer version of the same peptide has been shown to bind with a Kd of 70 nm
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-5 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.967, 119.967, 64.596
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Moesin / Membrane-organizing extension spike protein


Mass: 41141.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSN / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P26038
#2: Protein/peptide CD44 antigen / CDw44 / Epican / Extracellular matrix receptor III / ECMR-III / GP90 lymphocyte homing/adhesion ...CDw44 / Epican / Extracellular matrix receptor III / ECMR-III / GP90 lymphocyte homing/adhesion receptor / HUTCH-I / Heparan sulfate proteoglycan / Hermes antigen / Hyaluronate receptor / Phagocytic glycoprotein 1 / PGP-1 / Phagocytic glycoprotein I / PGP-I


Mass: 973.233 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Octapeptide based on the intracellular C-terminal tail of CD44
Source: (synth.) Homo sapiens (human) / References: UniProt: P16070
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M potassium thiocyanate, 0.1M bis-tris pH 7.0, 10% ethylene glycol, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→84.83 Å / Num. obs: 23382 / % possible obs: 99.7 % / Redundancy: 23.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.048 / Rrim(I) all: 0.173 / Χ2: 0.9 / Net I/σ(I): 11.1
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 11.7 % / Rmerge(I) obs: 3.189 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1977 / CC1/2: 0.46 / Rpim(I) all: 1.372 / Rrim(I) all: 3.492 / Χ2: 0.82 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E5W

1e5w


Resolution: 2.2→84.83 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.263 / WRfactor Rwork: 0.215 / SU B: 11.746 / SU ML: 0.264 / Average fsc free: 0.7371 / Average fsc work: 0.7584 / Cross valid method: FREE R-VALUE / ESU R: 0.275 / ESU R Free: 0.225
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2758 1034 4.439 %
Rwork0.2322 22259 -
all0.234 --
obs-23293 99.318 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 61.379 Å2
Baniso -1Baniso -2Baniso -3
1--2.521 Å20 Å20 Å2
2---2.521 Å20 Å2
3---5.042 Å2
Refinement stepCycle: LAST / Resolution: 2.2→84.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 0 0 39 2944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132962
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172919
X-RAY DIFFRACTIONr_angle_refined_deg1.471.6513975
X-RAY DIFFRACTIONr_angle_other_deg1.2171.5936730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.965346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06622.733172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47315596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1091521
X-RAY DIFFRACTIONr_chiral_restr0.0570.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023288
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02694
X-RAY DIFFRACTIONr_nbd_refined0.210.2584
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.22551
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21368
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21519
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.271
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.240.29
X-RAY DIFFRACTIONr_nbd_other0.1860.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.25
X-RAY DIFFRACTIONr_mcbond_it4.7696.0751390
X-RAY DIFFRACTIONr_mcbond_other4.776.0741389
X-RAY DIFFRACTIONr_mcangle_it6.669.1091734
X-RAY DIFFRACTIONr_mcangle_other6.6589.111735
X-RAY DIFFRACTIONr_scbond_it5.1046.6631572
X-RAY DIFFRACTIONr_scbond_other5.1036.6631572
X-RAY DIFFRACTIONr_scangle_it7.8169.7042241
X-RAY DIFFRACTIONr_scangle_other7.8169.7042241
X-RAY DIFFRACTIONr_lrange_it9.83268.1573236
X-RAY DIFFRACTIONr_lrange_other9.8368.1733236
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.2-2.2570.34900.43415700.42817310.3550.31395.89830.438
2.257-2.3190.394670.3716140.37116870.3130.33499.64430.364
2.319-2.3860.347590.35715770.35616360.4880.4841000.342
2.386-2.460.382950.34714720.34915670.6470.6511000.328
2.46-2.540.318720.34114340.3415170.6620.70799.27490.316
2.54-2.6290.276640.28314330.28315100.8320.82499.13910.259
2.629-2.7280.368490.2613790.26414440.8180.86898.8920.229
2.728-2.840.335740.25513030.25813930.8260.87398.85140.229
2.84-2.9660.368660.24512330.25113100.8620.88599.16030.222
2.966-3.110.272550.24312100.24412690.8840.8999.68480.224
3.11-3.2780.368370.24411760.24812160.860.89699.75330.227
3.278-3.4770.267300.24911110.2511430.8750.90299.8250.24
3.477-3.7170.34390.24410290.24810690.8460.89299.90650.236
3.717-4.0140.246460.2029840.20410320.9280.93299.80620.198
4.014-4.3960.196450.1718630.1729090.9490.95599.890.171
4.396-4.9130.175320.1548050.1558370.9560.9641000.156
4.913-5.670.31550.2127120.2197670.9130.931000.213
5.67-6.9360.323260.2245980.2286240.8540.9271000.224
6.936-9.7770.207180.1634790.1654980.9640.9699.79920.169
9.777-84.830.158150.2172770.2132920.9650.9571000.23

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